PXD002053

PXD002053 is an original dataset announced via ProteomeXchange.

Title	Breast cancer exosome protein profiling using TMT quantitation and SVM analysis
Description	Exosomes are microvesicles of endocytic origin constitutively released by multiple cell types into the extracellular environment. With evidence that exosomes can be detected in the blood of patients with various onco-malignancies, the development of a platform that uses exosomes as a diagnostic tool has been proposed. However, it has been difficult to truly define the exosome proteome due to the challenge of discerning contaminant proteins that may be identified via mass spectrometry using various exosome enrichment strategies. To better define the exosome proteome in breast cancer, we incorporated a combination of Tandem-Mass-Tag (TMT) quantitative proteomics approach and Support Vector Machine (SVM) cluster analysis of three conditioned media derived fractions corresponding to a 10,000 x g cellular debris pellet, a 100,000 x g crude exosome pellet, and an Optiprep enriched exosome pellet. In our TMT analysis, we identified and quantified 2,179 proteins in all three fractions, with known exosomal cargo proteins displaying at least a 2-fold enrichment in our exosome fraction based on our TMT protein ratios. Employing SVM cluster analysis allowed us to classify 241 proteins as “true” exosomal cargo proteins. Annotation tools revealed breast cancer derived exosomes were enriched in plasma membrane proteins with functional roles in cell adhesion and cell immunity, in addition to several cell signaling components. This study provides a robust and vigorous framework for the future development of using exosomes as potential multi-protein marker phenotyping tool in breast cancer diagnosis.
HostingRepository	PRIDE
AnnounceDate	2015-10-02
AnnouncementXML	Submission_2015-10-02_03:36:28.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	David Clark
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-04-13 01:46:58	ID requested
⏵ 1	2015-10-02 03:36:29	announced

Clark DJ, Fondrie WE, Liao Z, Hanson PI, Fulton A, Mao L, Yang AJ, Redefining the Breast Cancer Exosome Proteome by Tandem Mass Tag Quantitative Proteomics and Multivariate Cluster Analysis. Anal Chem, 87(20):10462-9(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, breact cancer, exosomes, TMT quantitation

Austin Yang
contact affiliation	University of Maryland School of Medicine Department of Anatomy and Neurobiology Marlene and Stewart Greenebaum Cancer Center
contact email	ayang@som.umaryland.edu
lab head
David Clark
contact affiliation	UMB School of Dentistry
contact email	david.clark@umaryland.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002053
     1. Label: PRIDE project
     2. Name: Breast cancer exosome protein profiling using TMT quantitation and SVM analysis